Mercurial > repos > galaxyp > metaquantome
changeset 3:28180bbb8fe4 draft
planemo upload commit 3762c462ff510cccd856f4ccd7fb87c44ad9b4e7
author | galaxyp |
---|---|
date | Thu, 06 Dec 2018 08:50:19 -0500 |
parents | a8cb3dea93a6 |
children | 80ce9ca55697 |
files | metaquantome_filter.xml metaquantome_viz.xml test-data/go_filtered.tab test-data/samples.tab test-data/tax_filt.tab test-data/tax_ns.png |
diffstat | 6 files changed, 59 insertions(+), 1 deletions(-) [+] |
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--- a/metaquantome_filter.xml Wed Dec 05 14:52:54 2018 -0500 +++ b/metaquantome_filter.xml Thu Dec 06 08:50:19 2018 -0500 @@ -76,6 +76,28 @@ <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/> <expand macro="output_samples"/> </outputs> + <tests> + <test> + <param name="expand_file" value="go_expanded.tab" ftype="tabular"/> + <param name="mode" value="f" /> + <param name="ontology" value="go" /> + <param name="samps_src" value="build" /> + <repeat name="samps"> + <param name="group_name" value="s1"/> + <param name="col_names" value="int1,int2,int3"/> + </repeat> + <repeat name="samps"> + <param name="group_name" value="s2"/> + <param name="col_names" value="int4,int5,int6"/> + </repeat> + <param name="min_peptides" value="1" /> + <param name="min_pep_nsamp" value="1" /> + <param name="min_children_non_leaf" value="2" /> + <param name="min_child_nsamp" value="1" /> + <param name="qthreshold" value="2" /> + <output name="outfile" file="go_filtered.tab" ftype="tabular"/> + </test> + </tests> <help><![CDATA[ TODO: Fill in help. ]]></help>
--- a/metaquantome_viz.xml Wed Dec 05 14:52:54 2018 -0500 +++ b/metaquantome_viz.xml Thu Dec 06 08:50:19 2018 -0500 @@ -99,7 +99,7 @@ help=""/> <conditional name="plot"> <param argument="--plottype" type="select" label="Plot type"> - <option value="bar">Bar Charti (bar)</option> + <option value="bar">Bar Chart (bar)</option> <option value="volcano">Volcano Plot (volcano)</option> <option value="heatmap">Heatmap (heatmap)</option> <option value="pca">Principal Componets Analysis (pca)</option> @@ -173,6 +173,22 @@ <outputs> <data format="png" name="outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="outfile.png"/> </outputs> + <tests> + <test> + <param name="infile" value="tax_filt.tab" ftype="tabular"/> + <param name="mode" value="t" /> + <param name="samps_src" value="history" /> + <param name="samps_file" value="samples.tab" ftype="tabular"/> + <param name="plottype" value="bar" /> + <param name="target_rank" value="genus" /> + <param name="meancol" value="NS_mean" /> + <param name="nterms" value="3" /> + <param name="barcol" value="1" /> + <param name="width" value="3" /> + <param name="height" value="3" /> + <output name="outfile" file="tax_ns.png" ftype="png" compare="sim_size" delta="50000"/> + </test> + </tests> <help><![CDATA[ TODO: Fill in help. ]]></help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/go_filtered.tab Thu Dec 06 08:50:19 2018 -0500 @@ -0,0 +1,2 @@ +id name namespace s1_mean s2_mean int1 int2 int3 int4 int5 int6 int1_n_peptide int2_n_peptide int3_n_peptide int4_n_peptide int5_n_peptide int6_n_peptide int1_n_samp_children int2_n_samp_children int3_n_samp_children int4_n_samp_children int5_n_samp_children int6_n_samp_children +GO:0008150 biological_process biological_process 10.066537719931583 11.4814630999144 10.011227255423254 10.287712379549447 9.868822554774999 11.782998208920414 10.9901039638575 11.560332834212444 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples.tab Thu Dec 06 08:50:19 2018 -0500 @@ -0,0 +1,3 @@ +group colnames +NS X737NS,X852NS,X867NS +WS X737WS,X852WS,X867WS \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tax_filt.tab Thu Dec 06 08:50:19 2018 -0500 @@ -0,0 +1,15 @@ +id taxon_name rank NS_mean WS_mean X737NS X737WS X852NS X852WS X867NS X867WS X737NS_n_peptide X737WS_n_peptide X852NS_n_peptide X852WS_n_peptide X867NS_n_peptide X867WS_n_peptide X737NS_n_samp_children X737WS_n_samp_children X852NS_n_samp_children X852WS_n_samp_children X867NS_n_samp_children X867WS_n_samp_children +712 Pasteurellaceae family 26.45508515455985 24.240760984631766 24.965005542520593 22.218244926365948 0.0 17.341365183225566 27.1723016809798 25.697827115441516 12.0 12.0 0.0 1.0 12.0 12.0 1.0 1.0 0.0 0.0 1.0 1.0 +724 Haemophilus genus 26.043545589333238 24.308669239875652 23.49238493402781 21.57274687722112 0.0 0.0 26.91490217583963 25.19610989120677 5.0 5.0 0.0 0.0 5.0 5.0 1.0 1.0 0.0 0.0 1.0 1.0 +729 Haemophilus parainfluenzae species 23.516051135977808 21.837453207025035 22.113077280032016 20.132830444840515 0.0 0.0 24.21369255243491 22.597204359627263 4.0 4.0 0.0 0.0 4.0 4.0 0.0 0.0 0.0 0.0 0.0 0.0 +1224 Proteobacteria phylum 26.506407720117732 26.405669726384243 25.647561843048845 25.684049762573892 25.572526514273356 26.02079872568725 27.451384780869606 27.10853680624065 18.0 18.0 3.0 4.0 17.0 17.0 2.0 2.0 2.0 2.0 2.0 2.0 +1239 Firmicutes phylum 28.512385596646148 30.091433318476454 28.16821189186139 29.85860894014845 28.689295147943678 29.902989443795985 28.625794429436656 30.43794314029389 247.0 362.0 325.0 366.0 317.0 354.0 3.0 2.0 3.0 3.0 3.0 2.0 +1301 Streptococcus genus 26.867617254051414 28.85011386863358 26.46624241376839 28.05891048314316 26.560458646377878 29.13539355848514 27.388297546047863 29.117339967272912 67.0 124.0 96.0 127.0 111.0 124.0 2.0 3.0 3.0 3.0 2.0 3.0 +1302 Streptococcus gordonii species 24.686370636745576 27.653507330007766 23.762400434698712 26.151624056996113 24.539475551766014 27.515752990669643 25.336906564014722 28.450914623490767 24.0 43.0 29.0 44.0 44.0 45.0 0.0 0.0 0.0 0.0 0.0 0.0 +28216 Betaproteobacteria class 23.29428542923752 24.791799066973446 22.374889513201293 21.402137416070087 24.544202571791207 23.84100698984557 19.8675358581728 26.047141520330538 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 +29465 Veillonella genus 27.14677305830786 28.768830375331426 27.034861383116564 28.980840680293607 27.47904567128595 27.71387087737904 26.85278433596802 29.212848758443123 134.0 167.0 149.0 156.0 126.0 156.0 3.0 2.0 3.0 2.0 2.0 3.0 +29466 Veillonella parvula species 18.832221452467913 23.646622731934286 18.99584905472981 22.846993959159153 18.647632848343047 21.527044665274683 0.0 24.781099201499504 3.0 4.0 2.0 4.0 0.0 4.0 0.0 0.0 0.0 0.0 0.0 0.0 +39778 Veillonella dispar species 20.06805764601431 21.234364824902784 18.873358040924337 21.41636590750601 18.430484676034965 0.0 21.232667529959397 21.02604333055197 4.0 4.0 1.0 0.0 4.0 4.0 0.0 0.0 0.0 0.0 0.0 0.0 +40674 Mammalia class 18.71423436046836 17.946348342079197 17.822232855425355 17.738850060395933 18.41771660331577 18.769965187049696 19.43400368663769 16.48885357307721 1.0 1.0 2.0 2.0 2.0 1.0 0.0 0.0 1.0 1.0 1.0 1.0 +46124 Granulicatella adiacens species 25.44795951209062 24.095117178766355 22.413021529130273 23.066852858599482 26.121087214932714 23.994120320785946 25.808003124552783 24.75258507306872 12.0 25.0 31.0 31.0 33.0 29.0 0.0 0.0 0.0 0.0 0.0 0.0 +186826 Lactobacillales order 27.515198585571607 29.11785831796523 26.715706855135487 28.32187712752904 27.586822118206747 29.36333727974101 27.974157758353318 29.426524865028252 92.0 171.0 151.0 183.0 167.0 176.0 2.0 3.0 3.0 3.0 2.0 3.0